[Bioclusters] help

Chris Dagdigian dag at sonsorol.org
Tue Jan 24 13:05:49 EST 2006


I still host some random intro level "bioIT" or "biocluster"  stuff  
posted at http://bioteam.net/dag/ that may provide some background  
info on life science clusters and the distributed resource management  
software that runs on them.

Software is harder. Most people do not run tools "which work only in  
cluster computing". The most common use case is for people to take  
programs that run on any old unix machine and install them on  
clusters so that they can run the program many times on many machines  
in order to solve a large serial or batch computing problem.  
Basically many people use clusters in bioinformatics as a way of  
massively increasing *throughput* of plain, generic, non-parallel  
codes applications and algorithms.

For "cluster only" software you'd have to look at MPI-enabled  
applications like: mpiblast and the variants of paup and MrBayes  
compiled for MPI environments.  There are a number of these programs,  
some free and some commercial. In general though, for bioinformatics  
you are not going to see very many MPI-enabled applications in daily  

There are some people on the beowulf mailing list who publish good  
stuff on http://www.clustermonkey.net/ and http://www.linuxhpc.org


On Jan 24, 2006, at 5:36 AM, ravi shankar wrote:

> Respected sir/madam
>                                     I Shankar.R doing  
> M.sc.Bioinformatics final year in Sri Ramachandra  Medical College   
> and Research Institute.chennai.INDIA...
>                                      I am currently working  on a  
> project "cluster computing for Bioinformatics" in LINUX  enviroment 
> (redhat 9.0) .Please let me know is there any free software   
> available for cluster computing and list of Bioinformatics tools  
> which  works only in cluster computing..
>                                      Eagerly waiting for the reply...
>   with regards
>   shankar

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